align

type Alignment interface {
	AddSequence(name string, sequence string, comment string) error
	AddSequenceChar(name string, sequence []rune, comment string) error
	GetSequence(name string) (string, bool)
	GetSequenceChar(ith int) ([]rune, bool)
	GetSequenceName(ith int) (string, bool)
	SetSequenceChar(ithAlign, ithSite int, char rune) error
	Iterate(it func(name string, sequence string))
	IterateChar(it func(name string, sequence []rune))
	IterateAll(it func(name string, sequence []rune, comment string))
	NbSequences() int
	Length() int
	ShuffleSequences()
	ShuffleSites(rate float64, roguerate float64) []string
	SimulateRogue(prop float64, proplen float64) ([]string, []string)
	RemoveGaps(cutoff float64)
	Sample(nb int) (Alignment, error)
	BuildBootstrap() Alignment
	Entropy(site int, removegaps bool) (float64, error) // Entropy of the given site
	Swap(rate float64)
	Recombine(rate float64, lenprop float64)
	Rename(namemap map[string]string)
	Pssm(log bool, pseudocount float64, normalization int) (pssm map[rune][]float64, err error) // Normalization: PSSM_NORM_NONE, PSSM_NORM_UNIF, PSSM_NORM_DATA
	TrimNames(size int) (map[string]string, error)
	TrimSequences(trimsize int, fromStart bool) error
	AppendSeqIdentifier(identifier string, right bool)
	AvgAllelesPerSite() float64
	CharStats() map[rune]int64
	Alphabet() int
	AlphabetCharacters() []rune
	Clone() (Alignment, error)
}

type Sequence interface {
	Sequence() string
	SequenceChar() []rune
	Name() string
	Comment() string
}